I have a 01 Prius and starts up then shuts off with check eng. on WHAT CAN I do? It looks like don't switch to charge the main batt.
Judging by the extensive information we have to work with I would say have the vehicle transportedlane: to a dealer.
If it does not run, then you need a flatbed tow to you-know-where. If it does run and sound normally, you can drive yourself there. When you arrive mention to them technical service bulletin EG011-03, and the possibility of soot interfering with the motion of the throttle butterfly. Those are my best guesses from you posting, but they are only guesses. We certainly hope there is no main battery problem; they are much more rare than the above.
